[Pw_forum] Reg: error while running tetra_example in PHonon examples in 6.1 version

Mitsuaki Kawamura mkawamura at issp.u-tokyo.ac.jp
Tue Apr 25 06:42:14 CEST 2017


Dear Dr. P.V.SREENIVASA REDDY

The tetrahedron method in the DFPT calculation works only together with the "New XML I/O" module.
However this I/O module is not activated in the default configuration. Therefore, please build QE as
$ ./configure --enable-xml
$ make
I am sorry for my too short information in the previous e-mail.

Activation of the new XML I/O will become the default setting in the next version which will be released sooner or later.

Best regards,
Mitsuaki Kawamura

--
------------------------------------------------------
Dr. Mitsuaki Kawamura
Software Advancement Team
Supercomputer Section
Materials Design and Characterization Laboratory
The Institute for Solid State Physics, Kashiwa, Japan
e-mail : mkawamura at issp.u-tokyo.ac.jp
------------------------------------------------------

From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On Behalf Of Peram sreenivasa reddy
Sent: Tuesday, April 25, 2017 1:07 PM
To: PWSCF Forum <pw_forum at pwscf.org>
Subject: [Pw_forum] Reg: error while running tetra_example in PHonon examples in 6.1 version

Dear PWSCF,
I am trying new 6.1 version of PWSCF for phonon calculations.
I am trying to run the examples inside PHonon/tetra_example for aluminium.
Here i am giving my complete input.

#!/bin/bash
#PBS -N teat_al  
#PBS -q workq
#PBS -l select=1:ncpus=1:mpiprocs=16:ompthreads=1

DEVICE="mlx4_0" #connectX3
PORT="1"

# FCA
#export OMPI_MCA_coll_fca_enable="1"
#export OMPI_MCA_coll_fca_np="0"
#FCAOPTIONS="-x fca_ib_dev_name=${DEVICE}"


export OMPI_MCA_btl_openib_if_include="${DEVICE}:${PORT}"
export OMPI_MCA_mpi_paffinity_alone="1"
export OMPI_MCA_rmaps_base_schedule_policy="slot"
export OMPI_MCA_btl_openib_use_message_coalescing="1"
export OMPI_MCA_rmaps_base_dist_hca="${DEVICE}:${PORT}"
export OMPI_MCA_btl="self,openib,sm"

# MXM
export OMPI_MCA_pml="cm"
export OMPI_MCA_mtl="mxm"
export OMPI_MCA_mtl_mxm_np="0"

MXMOPTIONS="-x MXM_RDMA_PORTS=${DEVICE}:${PORT}"
MXMOPTIONS="$MXMOPTIONS -x MXM_TLS=ud,shm,self -x MXM_SHM_RNDV_THRESH=32768 -x KMP_BLOCKTIME=0"

cd $PBS_O_WORKDIR

cat $PBS_NODEFILE | sort    > hostfile.pbs
cat $PBS_NODEFILE | sort -u > nodefile.pbs
sed -e "s/.bmc.pdb.local//g" -i nodefile.pbs
HOSTFILE=nodefile.pbs

PPN=1
TMP_DIR=/home/kanchana/sreenivas/pwscf/SnP/PH_test_with_6.1/tetra_example/test1/TMP
mpirun=/opt/apps/openmpi/intel/bin/mpirun
exe_pw=/home/kanchana/QE_6.1/qe-6.1/bin/pw.x
exe_ph=/home/kanchana/QE_6.1/qe-6.1/bin/ph.x
exe_dy=/home/kanchana/QE_6.1/qe-6.1/bin/dynmat.x
exe_al2f=/home/kanchana/QE_6.1/qe-6.1/bin/alpha2f.x
number_of_cores=1


#
#  SCF at k-mesh good enough for phonons
#
cat > al.scf.in << EOF
&CONTROL
 calculation = 'scf' ,
    prefix='aluminum',
    pseudo_dir = '/opt/apps/pseudo',
    outdir='$TMP_DIR/'
/
&SYSTEM
       ibrav = 2,
   celldm(1) = 7.628216862d0,
         nat = 1,
        ntyp = 1,
     ecutwfc = 40.0 ,
     ecutrho = 150 ,
 occupations = 'tetrahedra_opt' ,
/
 &ELECTRONS
/
ATOMIC_SPECIES
 Al   26.98000  Al.pbe-n-rrkjus_psl.0.1.UPF
ATOMIC_POSITIONS alat 
 Al      0.000000000    0.000000000    0.000000000    
K_POINTS automatic 
 8 8 8 0 0 0
EOF
time -p ${mpirun} --bind-to core -n $number_of_cores --map-by ppr:$PPN:node \
                        -x MLX5_SINGLE_THREADED=1 \
                        -x MLX5_STALL_NUM_LOOP=0 ${MXMOPTIONS} ${FCAOPTIONS} \
                        ${exe_pw} -input al.scf.in > al.scf.out 2>&1

#
# Phonon calculation
#
cat > al.ph.in << EOF
Al phonon
&INPUTPH
   prefix = 'aluminum',
   outdir = '$TMP_DIR/',
   fildyn = 'al.dyn'
 fildvscf = 'dv',
  fildrho = 'drho',
    ldisp = .true.,
 lshift_q = .true.,
      nq1 = 2, 
      nq2 = 2,
      nq3 = 2,
/
EOF

time -p ${mpirun} --bind-to core -n $number_of_cores --map-by ppr:$PPN:node \
                        -x MLX5_SINGLE_THREADED=1 \
                        -x MLX5_STALL_NUM_LOOP=0 ${MXMOPTIONS} ${FCAOPTIONS} \
                        ${exe_ph} -input al.ph.in > al.ph.out 2>&1

#
# Electron-phonon calculation
#
cat > al.elph.in << EOF
Al electron-phonon
&INPUTPH
          prefix = 'aluminum',
          outdir = '$TMP_DIR/',
          fildyn = 'al.dyn'
        fildvscf = 'dv',
         fildrho = 'drho',
           ldisp = .true.,
        lshift_q = .true.,
             nq1 = 4, 
             nq2 = 4,
             nq3 = 4,
 electron_phonon = "lambda_tetra"
             nk1 = 16,
             nk2 = 16,
             nk3 = 16,
/
EOF
time -p ${mpirun} --bind-to core -n $number_of_cores --map-by ppr:$PPN:node \
                        -x MLX5_SINGLE_THREADED=1 \
                        -x MLX5_STALL_NUM_LOOP=0 ${MXMOPTIONS} ${FCAOPTIONS} \
                        ${exe_ph} -input al.elph.in > al.elph.out 2>&1


#
# Eliashberg function
#
cat > lambda.in << EOF
&input
      ne = 500, 
  ltetra = 2, 
  fildyn = "al.dyn", 
  mustar = 0.1, 
  prefix = "$TMP_DIR/aluminum",
/
EOF
time -p ${mpirun} --bind-to core -n $number_of_cores --map-by ppr:$PPN:node \
                        -x MLX5_SINGLE_THREADED=1 \
                        -x MLX5_STALL_NUM_LOOP=0 ${MXMOPTIONS} ${FCAOPTIONS} \
                        ${exe_al2f} -input lambda.in > lambda.out 2>&1
----------------------------
it works fine for pw.x and it created al.scf.out file. But when it came to run al.ph.in file it is giving error like bellow.


     Program PHONON v.6.1 (svn rev. 13369) starts on 25Apr2017 at  9:25:11 

     This program is part of the open-source Quantum ESPRESSO suite
     for quantum simulation of materials; please cite
         "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
          URL http://www.quantum-espresso.org", 
     in publications or presentations arising from this work. More details at
     http://www.quantum-espresso.org/quote

     Parallel version (MPI), running on     1 processors

     Reading data from directory:
     /home/kanchana/sreenivas/pwscf/SnP/PH_test_with_6.1/tetra_example/test1/TMP/aluminum.save

   Info: using nr1, nr2, nr3 values from input

   Info: using nr1, nr2, nr3 values from input
MXM: Got signal 11 (Segmentation fault)
==== backtrace ====
    0  /lib64/libc.so.6(+0x32920) [0x2adc149bd920]
    1  /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x8f8b0d]
    2  /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x6c1add]
    3  /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x6be3ec]
    4  /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x6c9aa3]
    5  /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x48617b]
    6  /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x40f5b9]
    7  /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x40f53c]
    8  /lib64/libc.so.6(__libc_start_main+0xfd) [0x2adc149a9cdd]
    9  /home/kanchana/QE_6.1/qe-6.1/bin/ph.x() [0x40f439]
===================
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 25670 on node compute0 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
it seems to be fail to read the previous output files from TMP folder.
I am using the same input as given in the example. but still getting errors.
Please suggest any suggestions?

Thanking you.




-- 
P.V.SREENIVASA REDDY
Research Scholar
Department of Physics
Indian Institute of Technology
Hyderabad





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